Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes

Frontiers in Microbiology
Hirokazu TojuShinji Fukuda

Abstract

Constructing biological communities is a major challenge in both basic and applied sciences. Although model synthetic communities with a few species have been constructed, designing systems consisting of tens or hundreds of species remains one of the most difficult goals in ecology and microbiology. By utilizing high-throughput sequencing data of interspecific association networks, we here propose a framework for exploring "functional core" species that have great impacts on whole community processes and functions. The framework allows us to score each species within a large community based on three criteria: namely, topological positions, functional portfolios, and functional balance within a target network. The criteria are measures of each species' roles in maximizing functional benefits at the community or ecosystem level. When species with potentially large contributions to ecosystem-level functions are screened, the framework also helps us design "functional core microbiomes" by focusing on properties of species groups (modules) within a network. When embedded into agroecosystems or human gut, such functional core microbiomes are expected to organize whole microbiome processes and functions. An application to a plant-asso...Continue Reading

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Citations

Oct 26, 2020·Microbial Biotechnology·Maria L Marco
Mar 13, 2021·Nature Communications·Ignacio BeldaIsak S Pretorius
Apr 8, 2021·Current Opinion in Plant Biology·Maria J PozoAinhoa Martinez-Medina
Jun 23, 2021·Microbial Biotechnology·Bruna D Batista, Brajesh K Singh
Oct 2, 2021·Frontiers in Microbiology·Yoshie HoriHirokazu Toju

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Datasets Mentioned

BETA
DRA010262

Methods Mentioned

BETA
amplicon sequencing
Illumina
Illumina sequencing
PCR
chips

Software Mentioned

bcl2fastq
FUNGuild
SpiecEasi
FAPROTAX
R
Spiec
R scripts
Easi
DADA2
igraph

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